Terapon jarbua is a commercially important coastal water fish widely distributed across the Indo-West pacific region. To assess the genetic diversity and population structure of this species in the coastal waters of China, sequence variation in 962 base pairs of the mitochondrial DNA control region (CR) of 102 individuals from five populations were analyzed. In total, 205 polymorphic sites defined 102 haplotypes. High levels of genetic diversity (total nucleotide diversity Pi was 0.022 ±0.002, ranged from 0.014 in Pingtan to 0.028 in Boao) and no significant genetic differentiation (Fst=-0.014-0.041, P > 0.005) were observed. The significantly negative value of Fu's Fs (-23.961, P < 0.001) suggested a T. jarbua population expansion of approximately 0.169-0.051 Ma BP in the coastal waters of China. The neighbor-joining tree and haplotype network revealed the existence of three monophyletic matrilineal lineages, with an inter-lineage genetic distance (range:0.024-0.031) considerably greater than that within lineages. Moreover, a remarkable genetic differentiation was observed among lineages (Fst=0.508-0.698, P < 0.001), the deduced divergence time among the three lineages was 1.07-0.24 Ma BP, which might have been caused by the historical isolation of sea basins in the glacial period of Pleistocene epoch. However, no such geographic structure was found, as the three lineages were composed of individuals from different localities. Lineage A comprised 85.3% of samples and showed a high level of genetic diversity (total nucleotide diversity was 0.012 ±0.001, ranged from 0.010 ±0.001 in Hepu to 0.014 ±0.001 in Pingtan). Pairwise Fst ranged from -0.022-0.068 (P > 0.005), and analysis of molecular variance showed only 1.97% variation among populations, indicated that genetic differentiation in Lineage A was not significant. Values of neutrality tests (Tajimas'D and Fu's Fs) of Lineage A were significantly negative (P < 0.001), and deduced population expansion time was approximately 0.254-0.076 Ma BP. The fluctuating sea levels and temperature during the period of mid-late Pleistocene might have caused divergence among these three lineages, and the secondary contact would have likely contributed to genetic homogeneity among different localities, resulted in a significant lineage structure but no geographical differentiation.